On Wed, Mar 26, 2014, Ilias Patmanidis wrote:
>
> I was using xleap to generate topology and coordinate files for a specific
> system
>
> >source leaprc.ff12SB
> >loadamberparams frcmod.ionsjc_tip3p
> >test = loadPDB test.pdb
> >addions test Na+ 2
> >solvatebox test TIP3PBOX 10
> >savePDB test test1.pdb
> >saveamberparm test test.prmtop test.crd
>
> Information about the vdw box size was missing from the end of the
> generated test.crd.
>
> This problem did not appear in tleap. The same commands gave a different
> output with the vdw box size included in the end of the file.
I cannot reproduce the problem. With xleap, I get the box info at the end of
the crd file. I really suspect operator error here: tleap and xleap share the
same code, and it is very hard to see how xleap and tleap could be giving
different answers. Also, if this simple workflow were failing, everyone on
the Amber list would be posting problem reports. Can you double-check that
you used exactly the same commands in xleap as in tleap?
Is the *only* difference between xleap and tleap the box info? Are the prmtop
files different at all?
...dac
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Received on Wed Mar 26 2014 - 11:00:03 PDT
